Advancements In Microfluidics For Biotechnology Applications

University of Minnesota Ph.D. dissertation. October 2018. Major: Chemical Engineering. Advisors: Theresa Reineke, Kevin Dorfman. 1 computer file (PDF); vii, 122 pages.Microfluidic technology has made a huge impact in the field of biotechnology and life sciences. The advancements can be categorized into three aspects: understanding of physical phenomena at the microscale; development of tools for easy integration of different phenomena; and devising systems for various applications. This thesis highlights the ability of microfluidic technology in manipulating different biological entities by fabricating small feature sizes. In particular, we have focused on the development of new processes for three biotechnology applications – (i) long DNA sample preparation for genomic; (ii) delivery of genetic delivery vehicles for gene and cell therapy; and (iii) an in vitro model to study human gut. Each of these systems is developed in close collaboration with potential users and is aimed towards easy integration with the existing workflow. Long-read genomic applications such as genome mapping in nanochannels require long DNA that is free of small-DNA impurities. Chapter 2 reports a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an externally applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivity of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies. Non-viral delivery vehicles are becoming a popular choice to deliver genetic materials for various therapeutic purposes, but they need engineering solution to improve and control the delivery process. In Chapter 3, we demonstrate a highly efficient method for gene delivery into clinically relevant human cell types, such as induced pluripotent stem cells (iPSCs) and fibroblasts, reducing the protocol time by one full day. To preserve cell physiology during gene transfer, we designed a microfluidic strategy, which facilitates significant gene delivery in short transfection time (<1 minute) for several human cell types. This fast, optimized and generally applicable cell transfection method can be used for rapid screening of different delivery systems and has significant potential for high-throughput cell therapy applications. Microfluidic in vitro models are being developed to mimic individual or combination of various human organ functions for systematic studies, and for better predictive models for clinical studies. In Chapter 4, we outline a microfluidic-based culture system to study host-pathogen interaction in the human gut. We demonstrate that the infection of Enterohemorrhagic Escherichia coli (EHEC) in epithelial cells are oxygen dependent and can be used to prolong co-culture of bacterial and epithelial cells. This work presents a large scope to study the factors influencing the infection, especially the commensal microbiome in the human gut. Overall, this thesis shows how the microfluidic system can be useful in solving real-life problems and envision further advancements in the field of biotechnology

Dynamic effects of harnessing cables on distributed parameter systems for space applications: Analytical modeling and experimental validation

Power and data signal cables constitute a major component of lightweight spacecraft and satellite structures. These cables can account for up to as high as 30% of the structural mass and hence significantly impact the structural dynamics. Until the last decade, these cables were primarily modeled using ad hoc techniques that considered cables as non-structural mass elements and neglected their stiffness and damping effects. However, in the last decade, accurate modeling of cable-harnessed structures has come into the spotlight by incorporating cable dynamics that are governed by cable's stiffness and damping in addition to its mass. Accuracy of these lightweight space structure models are important because the control systems heavily rely on them for their robust performance. Hence, the primary goal of this research is to create simple analytical models that can predict the accurate dynamic behavior of cable-harnessed structures. The beauty of analytical models lie in the fact that they result in low-order high-fidelity governing partial differential equations (PDE) and hence are advantageous over the numerical methods, such as finite element method. A reliable low-order PDE of a dynamical system ensures the robustness of the control algorithms. Additionally, analytical models provide deeper insights into the system due to the possibility of obtaining closed-form solutions and ease of conducting parametric analysis. The current research can be classified into solving the following two broad problems: 1. modeling the damping mechanisms in cable-harnessed beam structures, 2. modeling the accurate stiffness and inertia effects in cable-harnessed two-dimensional structures. The first problem addresses accurate modeling of material damping in the cable-harnessed beam system which was identified as a major gap in the present literature. The system consists of the cables wrapped around the beam in specific periodic geometry. In the presented research, the energy loss mechanisms in the system was incorporated by using the Kelvin-Voigt and hysteresis damping models. Applying an energy-equivalent homogenization method, the proposed technique modeled the cable-harnessed beam as an equivalent continuum (beam-like) structure. In order to validate the model, cable damping was first characterized using dynamic testing methods and relevant loss factors were obtained for both the models. In the next step, experimental modal testing was performed on the fabricated cable-harnessed beams to obtain the modal characteristics of the system such as natural frequencies and frequency response functions. These experimentally obtained characteristics were compared with those using the proposed model and were found to be in a good agreement. The second problem constitutes the major contribution of this thesis. It is worth mentioning that in the past, no analytical models have been developed that consider two-dimensional plate-like host structures to model the cable-harnessed system. Researchers have generally considered one-dimensional beam-like host structures for modeling purpose as it simplifies the mathematical formulation. In this research, analytical modeling based on a homogenization approach is proposed to develop an equivalent continuum model of cable-harnessed plates. This modeling problem is further broken down into the following sub-problems depending on the way the cables are harnessed to the host plates: 1. cables harnessed parallel to a plate's edge, and 2. cables wrapped across the plate in a defined pattern. For both these cases, separate mathematical derivations were carried out to obtain governing PDEs that represent the dynamic behavior of these structures. The proposed models are experimentally validated using modal testing of the fabricated cable-harnessed plates. Comparisons of natural frequencies, mode shapes and frequency response functions provided confidence in the correctness of the proposed model. In addition to providing accuracy for low order control algorithms, the proposed models can be further used to obtain optimal cable placement strategies such that the dynamic effects of the cable harness are minimized

A supramolecular strategy for ratiometric luminescence sensing of nitroaromatic explosives in water

In the present work we have demonstrated a supramolecular approach for ratiometric luminescence sensing of nitroaromatic explosive compounds (NAEs) by employing a red luminescent Eu(III) complex and a green luminescent Pt(II) complex with in a Triton X-100 surfactant based micellar host in water. The Eu-complex gets entrapped inside micellar core whereas the Pt-C2 remains grafted on the surface of the spherical micelles due to their structural amendments and thus facilitates preferential interaction of Pt-C2 with NAE molecules mainly through p-p interaction. The presence of explosive traces quenches the green emission (508-545 nm) of Pt-complex whereas the red emission (614 nm) of Eu-complex remains unaffected. The strategy demonstrates first report of two independent luminophore based ratiometric sensing in water using a micellar host

A supramolecular strategy for ratiometric luminescence sensing of nitroaromatic explosives in water

1814-1821In the present work we have demonstrated a supramolecular approach for ratiometric luminescence sensing of nitroaromatic explosive compounds (NAEs) by employing a red luminescent Eu(III) complex and a green luminescent Pt(II) complex with in a Triton X-100 surfactant based micellar host in water. The Eu-complex gets entrapped inside micellar core whereas the Pt-C2 remains grafted on the surface of the spherical micelles due to their structural amendments and thus facilitates preferential interaction of Pt-C2 with NAE molecules mainly through π-π interaction. The presence of explosive traces quenches the green emission (508-545 nm) of Pt-complex whereas the red emission (614 nm) of Eu-complex remains unaffected. The strategy demonstrates first report of two independent luminophore based ratiometric sensing in water using a micellar host